June 29, 2016 at 10:29 am #6346
Focus stacking (FS) is a software-assisted method for taking multiple images of a fossil (or other still life) at varied points of focus throughout the depth of the subject. In the final image, the subject seems to take on sharpness throughout. Ordinarily, the in-focus to out-of-focus transition conveys subtle cues about the size of the subject as well as its depth. You may be aware through experience that the closer you place your lens to the object you are photographing, the narrower the depth of focus you can obtain. For cameras that allow control of lens aperture, you can adjust the f-stop value to increase the depth of focus somewhat. Make the aperture too small (a high f-stop number) and you will experience diffraction — the softening of fine details.
Following the recent Cincinnati Mini-conference, I tested out Zerene Stacker on some of the fossil specimens collected/received on that trip. I plan to post a couple of the results in a follow-up post below. My FS technique is not perfect, but here are some practical requirements to get satisfactory results:
- A locked-down support platform, preferably a solid tripod
- Consistent and high-quality lighting on the subject
- Consistent exposure values (if your camera does not meter consistently, it may affect the quality of the finished image; revert to manual exposure control if necessary)
- Ability to repeatably adjust focus in very small increments
This last one may take the most patience and practice of all! At least half of my FS’ed images were made with focus increments that were too large. Thus, the finished image shows “bands” of alternation between sharp and slightly out-of-focus on the fossil. Live and learn.June 29, 2016 at 10:59 am #6347
Thanks Matthew (@matthew-croxton) for participating in that forum. The stacking method is something very useful and we already have an iDigBio video published with the stacking process as part of our best practices for getting high quality images. Check this: https://vimeo.com/160615629
Nevertheless I think it is very helpful to start that topic within our forum here. I would like to ask you if you maybe can create some workflow scheme about the process, with pictures and text? That would be great and we could upload it to our resources section.
What do you think?
RonnyJune 30, 2016 at 10:17 pm #6370
Here’s a coiled trilobite specimen captured using a focus stack of seven images.July 1, 2016 at 10:37 am #6378
Hey Matthew (@matthew-croxton), This looks very nice! Have you thought about the workflow scheme?
RonnyJuly 1, 2016 at 4:33 pm #6397
I’d enjoy making an illustrated tutorial. I’m evaluating grad studies in education and working out the details is consuming much of my spare time and creativity at the moment. I’m sure you can understand. When the pieces start to fall into place, then I’d like to continue participating by contributing!
Cheers!July 5, 2016 at 11:36 am #6400
Sure Matthew (@matthew-croxton) I understand. The more I appreciate your contributions. Whenever you will find some time for it
RonnyJuly 20, 2016 at 12:28 am #7083July 21, 2016 at 11:23 am #7090
are you talking about the stacking method??? There is a free software called CombineZP from Alan Hadley. http://alan-hadley.software.informer.com
It is for PC and quite simple. All you need to do is get images with different focus distance from your image (all with same length and height) and upload them to CombineZP
here is a short tutorial
have fun and let me know how it works
RonnyJuly 28, 2016 at 1:08 pm #7108
Yes, focus stacking was what I was referring to. I checked out the video link you sent and then a couple of others.
All methods seem to require a focusing rail. I checked those out on Amazon and read reviews. The under $100 versions all seem to suffer from creep unless used horizontally or only at a slight downward angle. All of my photos are taken straight down from a copy stand and it would seem that these inexpensive rails would not work well for me.
JackJuly 28, 2016 at 1:35 pm #7109
Hey Jack @jkallmeyer,
I had some good results just by using the manual focus of my camera. Btw. I am editing the video at the moment 😉
RonnyJuly 28, 2016 at 1:45 pm #7110
@jkallmeyer, I meant just to try how the stacking works. For really tiny objects (otoliths, foraminifera) I was always using my microscope with attached camera. I bought my vintage but supper nice preserved Bausch and Lomb Stereo Zoom 4 for about hundred bucks at eBay plus the adapter for the camera-ocular connection. Works fantastic!
RonnyJuly 28, 2016 at 9:10 pm #7111
I envy you! That microscope you bought was a real deal! I have always wanted one of those. Mine is a Swift with a two position lens that allows 10x and 20x settings plus, with the auxiliary lens, 15X and 30X. I use the 10x for cleaning and observing fossils about 90% of the time. I don’t have a camera adapter.
JackAugust 3, 2016 at 9:21 am #7122
Hey Jack (@jkallmeyer),
depending on the diameter of your ocular this adapter from AmScope might work. It’s the same one I use. It is definitely worth the price.
RonnyAugust 3, 2016 at 10:27 pm #7129
I checked out the Nikon version of this adapter. Amazon reviews are mixed. Does this device have optics in it? Reviewers said it doesn’t have a way to keep the camera from rotating when in use. Some say they had to rig spacers to keep the adapter from going too far in the microscope tube so they could focus. Some said the final photo image was not as sharp as what they saw through the microscope. Can you comment on any of this?
JackAugust 4, 2016 at 1:46 pm #7130
the adapter comes with the optics inside but you always will check the picture through the camera not through the microscope ocular but you have to adjust the focus with the microscope not with the camera zoom. But that is something you will have with any other optical device similar like that one. In my case it works well, no spacers needed. I can recommend it especially for the low price compared to other solutions.
RonnyAugust 4, 2016 at 10:15 pm #7132
Thanks Ronny. Your review is helpful.
JackAugust 19, 2016 at 12:03 pm #9448
I just saw your images of fossil gastropods in our fossil gallery and wondering why some are so yellowish. Is it because of the lighting or is it the real color??? However thanks for sharing these great findings.
RonnyAugust 26, 2016 at 10:56 pm #11092
Sorry for my delay in following through on a focus stacking forkflow. I moved and have just started school, so I’ve been very busy!
First, I’ll start with an example image that is a stack made of 12 images. Each image was manually focused using high magnification live view, and I still made mistakes in focusing too far between frames. “Over focusing” results in the strange areas of blurriness that you see when zoomed in to the full resolution. Some are indicated using black arrows, but there are still other areas blurred in just this small crop. So, the lesson to take from this exercise is that you should try and remove human error at every point possibleAugust 26, 2016 at 10:59 pm #11094
Now, here’s the closeup showing blurriness where detail should have been pixel-perfect if I’d moved through the focus range in smaller increments.August 26, 2016 at 11:43 pm #11096
I’m sorry! I realize this small piece of peacock ore is not a fossil. The reason I chose to use it is because I thought the highly-textured, iridescent surface would show off any focus errors clearly – and it does.
Here is some technical information on the shot:
Lens: 200mm macro, f/7.1, 1/4 s exposure for each frame. Once a correct exposure was determined, the camera was set to manual mode to insure that this exposure time and aperture remained constant through the dozen images. The shutter was released by timer for each shot, to minimize camera vibration.
Lighting: Two color-matched spotlights were used to illuminate ore, one to the left of the camera, and one to the right.
Staging: I didn’t have a pristine piece of neutral colored fabric available, so I just rested the ore on my leather wallet for the images.
- Images were imported into Adobe Lightroom. An initial color temperature and exposure adjustment was made to one image and then these settings were “synchronized” to all the others. Full size tiff files were exported from Lightroom.
- The tiff image files were imported into Zerene Stacker. A depth map method of stacking was chosen. This method requires the user to manually mask out areas which do not contain image detail using a slider for control. In the case of this image, much of the dark background was mapped out in the creation of the depth map.
- The stacked image that was output from Zerene Stacker was imported to Photoshop.
- In Photoshop, my first step was to tone down the brightness of highlight regions while also bringing up shadow areas ever so slightly. I used a method sometimes called the Picture Postcard Workflow (PPW). If you are serious about good color balance and realistic image enhancement, investing your time learning the resources and using the panel at http://www.moderncolorworkflow.com is worth the effort.
- My next step in Photoshop was to enhance the color separation in a natural way by using, and then backing off the Modern Man from Mars (MMM) technique. See the link above for explanation on how this approach works. There is also a book if you are interested in learning all the enhancements possible in the PPW. All require a fairly advanced level of comfort at working with layers in Photoshop, but none are gimmicks.
- In my final steps, I corrected a color cast in the shadow tones that was imparted during color enhancement, by using curves and measuring color values to assure that the wallet was the neutral black that I knew it to be. Lastly, I applied a black gradient across the left, right, and top side of the image to darken the background and better focus attention on the subject. A spot or two in the background was retouched.
I am attaching a single image from Lightroom, as it appeared prior to import into Zerene Stacker. It can serve as a “before” image for comparison to the final result.
You must be logged in to reply to this topic.